I agree that the train was likely an exercise in dramatic license. Given the quickness of Michael's departure, his destination and the secrecy surrounding his trip, and the utter lack of communication channels at that time, I don't think a plane would have been any more risk than the train. I also don't think the train would have been any less arduous from Tahoe/Reno to Miami, though there was far greater rail service in the 1950's than there is today. It simply would have been a long trip.
Michael could have have boarded the California Zephyr or the City of San Francisco, both of which served northern Nevada on their routes between the Bay Area and Chicago. While Amtrak serves Reno today, I can't say for certain that it would have been a stop along the route of the two most prominent west coast trains of the day. However, there were station stops a short drive from Reno east or west on the those rail lines. Either of those two trains would have carried him directly to Chicago where he would have boarded another train, possibly the Illinois Central's City of Miami or the Pennsylvania's Southwind, with direct service to Miami. It's also possible he may have made his way to San Francisco where he could have boarded the Southern Pacific's "Sunset Limited" from San Francisco to New Orleans making a connection in the Crescent City to Florida.
Since, in theory, nobody but Michael knew his final destination, he must have felt the secrecy of his trip coupled with the speed of his departure minimized his risk. Moreover, I can't imagine anyone would have guessed that Michael would have immediately left Tahoe bound for Miami and a meeting/confrontation with Hyman Roth.
None-the-less, by train from Northern Neveda connecting through Chicago to Miami, or connecting through New Orleans to Miami...I gotta think that's a four or five day trip!
tony b.